Arguably, that just means you can't pass laws that are directed towards / against religion. Not that religion is above the law. See Lemon Test: https://en.wikipedia.org/wiki/Lemon_v._Kurtzman#Lemon_test
According to this interpretation, church taxes (like the ones still present in some European countries) are unlawful, as is denying churches ability to gather their own donations. But churches still should pay same taxes that apply to other NGOs.